World Net Daily on “Expelled: No Intelligence Allowed”

Yeah, as if scientists were more dogmatics than you proponents of intelligent design.

As for the method use to obtain interviews for people as Myers…

Two thumbs down for Ben Stein.

Timothee,

There is a lot of disagreement here about ID. What isn’t allowed is dogmatism?

No. Dogmatism in science was really clearly defined by Robert Shapiro (also a reviewer of Behe’s “black box”, by the way) as the denial of the essential criteria of scientific thought : doubt.

I think it’s in the very early chapters of his book The Origins of Life, the one dealing with scientific methodology (according to me one of the best essay on the subject).

As he said, science is not a corpus of answer, but a way to find those answers. In my own conception of science, the results themselves are not science, because they are only the product of the methodology, not the process itself.

I guess that’s not the point. Dogmatism is the kind of behavior when someone refuses to see evidences against his view of the world. The most blatant example of dogmatism among proponents of ID is the use of the term “Darwinism”. There’s not such a thing as Darwinism! The theory of Darwin (it would be better to say “the model he proposed to explain evolution”) is only a theory, and I don’t know a single evolutionnist (and I know a huge number of them) who will look at a problem only with the ides of Darwin.
Scientists doesn’t believe in Darwin, nor they believe in Jay-Gould or Maynard-Smith. They believe in science, and truth (and cofee, more than anything else).
Tje only way for a scientist to find this truth is by looking at the facts. I don’t say that there is no dogmatism among scientist. I work sometimes with people engaged in systematics, and trust me, they are devoted to the ideas of their masters, and would never accept any other idea. Never, unless you bring them solid evidences that they are wrong.
That’s the problem with proponents of ID. The few examples you rely on (example: the flagellum who is displayed in this blog header) have been bunked out by science, but you still use them as proofs that evolutionnists are wrong. That’s dogmatism.

“I have four words for the producers and fans of Flock of Dodos:

Payback is a b*tch.”

***trying really hard not to laugh hysterically***

BTW, if anyone lives near Birmingham, Alabama, Expelled is going to have a huge rally before the debate between Richard Dawkins and John Lennox at the University of Alabama Birmingham.

Timothee,

Couple things.

1. How would you like to discuss the debunking of flagellum by science and we can see who is dogmatic here.

2. Since you say

“Scientists doesn’t believe in Darwin, nor they believe in Jay-Gould or Maynard-Smith. They believe in science, and truth”

What are the chances that this statement or a comparable statement be read at the beginning of every evolution section of every biology book sold/used in every public school and university in the US?

Let me hear about the non-dogmatic response to the acceptance of such a statement.

Timothee wrote, “No. Dogmatism in science was really clearly defined by Robert Shapiro (also a reviewer of Behe’s “black box”, by the way) as the denial of the essential criteria of scientific thought : doubt.”

Impressive. You set up the criteria for dogmatism the same way you set up the criteria for science. Anyone is disagrees with you is dogmatic.

Dogmatism is the arrogant assertion of opinion as fact, it has nothing to do with denial. For example, your definition of dogmatism is dogmatic. Not only is it opinion asserted as fact, it is flat out illogical. You make this logical error because you are so emotionally invested in Darwinism.

Timothee:

Dogmatism is the kind of behavior when someone refuses to see evidences against his view of the world.

But Timothee, that is what most evolutionary biologists do: they refuse to see evidence against their own theory. What about so-called “junk DNA”? It is highly conserved, and without any known function at this time. This is entirely in contradiction of Darwinian theory. You would think, based on the reaction of the biological community, as if these facts don’t exist. That’s, per your definition, “dogmatism”.

The most blatant example of dogmatism among proponents of ID is the use of the term “Darwinism”.

Are you kidding? Here’s what Wikipedia says about “Darwinism”:

“Darwinism is a term for the underlying theory in those ideas of Charles Darwin concerning evolution and natural selection.” Does that make Widipedia an ID resource?

. . . I don’t know a single evolutionnist (and I know a huge number of them) who will look at a problem only with the ides of Darwin.

Timothee, that’s encouraging. But, here in America (I’m positive you’re not from here) if you “doubt” Darwin’s theory, your career in biology is in terrible peril. Isn’t that what Dogmatists do, as in: ” work sometimes with people engaged in systematics, and trust me, they are devoted to the ideas of their masters, and would never accept any other idea. Never, unless you bring them solid evidences that they are wrong.”

Of course, here in the United States, Darwinists won’t accept any other idea even when you prove that they are wrong. Again, they’re dogmatists.

“That’s the problem with proponents of ID. The few examples you rely on (example: the flagellum who is displayed in this blog header) have been bunked out by science, but you still use them as proofs that evolutionnists are wrong. That’s dogmatism.”

So apparently, according to Timothee, we now know the step by step pathway for the evolution of the bacterial flagellum by RM+NS. Everyone will want to remember where they were on this day, at this moment in time. I’ll wait for a link to the press release (all the while not holding my breath).

The implications are staggering. What comes next? Empirical evidence of evolutionary pathways for vision, blood clotting, and of course all aspects of human and animal psychology can’t be far behind.

Evolution explains everything, of course, we just haven’t found any of the explanations yet. Give it time.

Honestly, what does NDE really even attempt to explain except for how a universe full of staggering complexity, purpose, and design can be the result of nothing more than a string of cosmic accidents?

Wait. Were we talking about Darwinism or dogmatism? They’re so easy to get confused.

@ jerry :

1. T3SS, plus the fact that 40 out of 42 proteins are used in other pathways, for a starter. We could engage in a “reference battle” (only PR journals of course), I’m trained (quite well) for that, as my field is rich in contrversials subjects.

2. It’s the first thing my teachers told me. It’s the only point of agreement i have with some evolutionnists. That’s also the first thing I say when someone tells me that a result is not coherent with his previous results. I’m also pretty sure to have read it in some evolution books. I mean, used in University and stuff…

@StephenB : I was talking of dogmatism in science. The denial of doubt, and the acceptance of facts without prudence seems a good definition to me. I’m not involved in Darwinism, by the way. Darwin’s theory don’t make any use of the works of, say, Mendel, and it’s quite a flaw in it. Anyway, just by observation, he defined what is still one (out of four) evolutionnary force: natural selection. Besides, I’m a scientist, I feel no emotion whatsoever for a theory. I eventually feel such a thing for the excitation of discovering new facts, of empathy with the animals I work with, but not for a conceptual object as Darwin’s theory is. The last time I felt something about Darwin was when I left his book felt on my bare foot by lack of cofee.

@PaV :

I must confess I have no answer to junk-DNA (and, despite a BSc in genomics, I don’t consider that I have enough knowledge of the subject to talk about it – and with my research going on, I have no time to digg into papers).

I can, however, see something like a structural role, or the presence of very distal elements, or elements involved in chemical regulation of chromatid structure. We don’t need to invoke a designer here. We need to carry out good science. Then find out. I’m pretty confident the “mystery” of junk-DNA will be solved in the next 5 years.

About Wikipedia : that’s not an encyclopedia. Don’t believe, it’s crappy. Trust me one this one, I used to wrote articles in it

Seriously. The word Darwinist is used for someone who trust the ideas of Charles, ok, right. So I’m a part-Darwinist. Because I read his books, compared with the newest evidences, read other people books, read a lot of papers, look at my results, look at other people results, talk with colleagues and friends, and made my own point of view.

I’m sure that any of the evolutionist in post (even in USA) is in agreement with Darwin on every word. Because it scientifically impossible, Darwin’s theory is 200 years old.

As you noticed, some people in systematics can be dogmatists. It’s easily explained by sociological analysis, or epistemology. It’s the nature of systematics to be dogmatic. But the most prominent systematicians in france are one of the most open-minded people I’ve ever heard of. And you will notice that I said : “Never, unless you bring them solid evidences that they are wrong”. We still are scientifics…

As for your last sentence: intelligent designers are yet to prove anything (and to be published in a peer-reviewed journal. Some of them exist outside US, so “local specificity” is a poor excuse). Inductivism or inference alone are not demonstrative.

@Apollos:

I don’t talked about a step-by-step pathway of evolution. Reconstructing step-by-step pathway is part of my research (even if it’s not sensu stricto pathways I’m reconstructing, but nevermind)

It’s just that the flagellum is a perfect exemple to show that a theory such as “irreducible complexity” is totally wrong. Because parts of the flagellum exists outside the flagellum, and are fully functionnal. I’m sure you’ve not read even the smallest paper on the subject. Am I right?

Let’s take a look at, say, oncogenic receptors, you will find out that biochemistry is all about using small functionnal units (proteic domains, for that matter) and modulate them in space to provide another function. And Michael Behe is aware of this fact, but he just refused to see it when writing is theory.

Anyway, we know step-by-step pathways for a lot of things far more amazing than the flagellum. In immunogenetics, for example - evolution of MHC genes, Ig complexes, and so on.

You’ll be surprised of the vast amount of knowledge we’ve gathered on the evolution of behaviors in animals. Open up pubmed / google scholar / ISI WoS and go find out by yourself.

And it’s not only “Darwinism” (NS). In fact, it’s a combination of the four major forces driving evolution (who in this topic can give me their name, by the way?), plus environment.

Who says “Darwinism”?

Darwinism
http://www.bringyou.to/apologetics/p45.htm

Michael Ruse: I am a Darwinian.
“Many contemporary Darwinists show a strong liberal commitment in their politics and sexual morality, whereas advocates of creation want to go back to a strict biblical morality.”
“Darwinism has a great past. Let us work to see that it has an even greater future.”

Live in debate:
But I do agree, I do hope that Darwinism does have a great future, and I hope that you and I can contribute together to do this.

Right. Yes, I think that Darwinism — Darwinism is a scientific theory. Of course I think —

Eugenie Scott:
“Darwinism, which is natural selection - evolution by natural selection”.

“ES: I’m finishing. Um, Darwinism — evolution by natural selection is one of the ways by which evolution can take place. The argument that has been presented so frequently from your side of the table is that if you — all we have to do is disprove Darwinism, and we disprove evolution. That’s nonsense. Another point, I will try to answer your question, I’m sorry — ”
=====
I’m a Darwinist because I believe the only alternatives are Lamarckism or God … ,
-Richard Dawkins

The real core of Darwinism … is the theory of natural selection. This theory is so important for the Darwinian because it permits the explanation of adaptation, the ‘design’ of the natural theologian, by natural means, instead of by divine intervention. (p. 138 Ernst Mayr (Foreword to M. Ruse, Darwinism Defended, Reading, Mass. Addison-Wesley, 1982, pp. xi-xii) )

… , it is simply not true that Darwinism works with any substrate, no matter what. Indeed Darwinism can’t even explain old-fashioned *biological* evolution if the hereditary substrate doesn’t behave just right. …This substrate problem was so acute that turn-ofthe-century biologists — all fans of blending inheritance — concluded that Darwinism just can’t work. ….” (Orr H.A., “Dennett’s Strange Idea: Natural Selection: Science of Everything, Universal Acid, Cure for the Common Cold … . Review of “Darwin’s Dangerous Idea,” by Daniel C. Dennett, Simon and Schuster. Boston Review, Vol. 21., No. 3., Summer 1996.)

http://post-darwinist.blogspot.....-away.html

Catholic biologist Ken Miller, author of Finding Darwin’s God, is introduced. “I’m an orthodox Catholic, and an orthodox Darwinist …
www.staycatholic.com/evolution.htm - 13k - Cached - Similar pages

Lynn Margulis: “It was like confessing a murder when I discovered I was not a neo-Darwinist.” But, she quickly added, “I am definitely a Darwinist though. I think we are missing important information about the origins of variation. I differ from the neo-Darwinian bullies on this point.”
http://www.pandasthumb.org/arc.....lis_d.html

1860 April The term “Darwinism” was coined by Thomas Huxley in the Westminster Journal
http://www.aboutdarwin.com/timeline/time_07.html

9. Richard Dawkins, “Darwin Triumphant: Darwinism as a Universal Truth,” in Michael H. Robinson and Lionel Tiger, eds., Man and Beast Revisited (Washington, DC: Smithsonian Institution Press, 1991), 38; also see Dawkins, The Blind Watchmaker, 317. … As Dawkins has stressed, discovery of “a single, well-verified mammal skull . . . in 500 million year-old rocks” would utterly destroy core Darwinism (The Blind Watchmaker, 225).
http://www.ndu.edu/inss/McNair.....52c8n.html

Darwinism and the expansion of evolutionary theory. SJ Gould. The essence of Darwinism lies in the claim that natural selection is a creative force, …
www.sciencemag.org/cgi/content.....6/4544/380

Ayala “Beyond Darwinism?” - RPB Ch 11. EI lab (Hubbard Hall G36) open for evolutionary …
www.msu.edu/~pennock5/courses/484Spring2007.htm

Mayr :“I’m an old-time fighter for Darwinism. I say, ‘Please tell me what’s wrong with Darwinism. I can’t see anything wrong with Darwinism.”
http://www.wsws.org/articles/2.....-m03.shtml

Confessions of a Darwinist

Niles Eldredge

It takes a true Darwinist to tweak the great man’s vision, bringing it into line with the facts of the matter. I confess that I am a true Darwinist.
http://www.vqronline.org/artic.....darwinist/

Timothee,

You will be hit with a lot of counterargumens and hopefully, you will stay around to sort them all out. We are well aware of the arguments proposed by Ken Miller and summarized by Nick Matzke about the flagellum.

Hopefully, on this or another thread a detailed discussion can take place.

The presence of the same proteins in other pathways is by no means a proof that they were available in one place at one time and then could have been assembled in so complex a manner. This assumes not only the concept of co-option but also a magical power of self assembly that can almost do anything one wants. This is sometimes called the argument from Mars approach and is best summed up by someone who is not necessarily a friend of ID. His name is David Opderbeck and here is his quote from the ASA site

“David C. said:* Co-option falsifies IC (irreducible complexity) because it provides a way to assemble the complex system step by step.*

Not so. In itself, co-option shows only that some components of a putatively IC system could possibly have been borrowed from some other system. It does
not, in itself, show how the entire system could have been assembled step-by-step such that there is some utility in the system at each step.

The possibility of co-option might suggest a system really isn’t IC, but it would have to be the case not only that there are coopt-able parts that would “fit” the system, but also that the putatively co-opted parts were available for co-option and that they could have been assembled all at once into the IC system. This requires both some kind of proximity as well as some possibility of self organization of the system. It isn’t enough to suggest that there is a small piece of metal on Mars that could be used as the catch bar in a mouse trap; you have to show that there is a small piece of metal in proximity to the other components and that there is a mechanism for spontaneous and complete self-assembly of the proximate parts into a system; or that there are intermediate systems to which proximately available parts could gradually be added, each of which intermediate systems has some utility.

So, to suggest that co-option in itself falsifies IC, it seems to me, is really just hand-waiving. Either that, or it really is a fundamental misunderstanding of what IC is supposed to mean.

Now, Ken Miller cites a bunch a papers that supposedly show a pathway in which the bacterial flagellum could have been assembled through gradual co-option of parts into the present motor system. But this is where it gets frustrating for someone like me: when you dig into the papers he cites, they don’t seem to support anything like such a grandiose claim. In some instances, it seems more like “well, there’s a little piece of metal on Mars that could serve as the catch on a mousetrap,” rather than any kind of meaningfully plausible scenario. (Either that, or my incompetence with the literature makes me — and Angus Menuge, from whose “Agents Under Fire” much of this rebuttal comes from — miss something.)

I do think it’s fair to say that the possibility of co-option suggests that something that *seems* to be IC *might* be derivable through natural selection after all, which I would agree should make us chary of grand claims for the concept of IC — certainly it should make us reject any claim that the concept of IC *must be* a show-stopper. However, it equally overstates the case, IMHO, to claim that the concept of co-option conclusively settles the matter against IC as a possible roadblock for natural selection. ”

If such an argument as co-option was presented in other fields they would laugh at you but in evolutionary biology it is the norm.

Timothee, I am curious. How would you characterize your scientific world view? Is it close to that of Stephen J. Gould? I know you disapprove of intelligent design and you seem skeptical about neo-Darwinism. Is there any well-known position that you identify with?

Timothee;
HMMM,
You seem to think Darwinism is in the bag,,,,I would like to know what you think is the most “CONCLUSIVE” proof or proofs for evolution…And then we can provide ample proof that will AT LEAST bring reasonable doubt if you are honest about it….SO let’s have it…What do you consider the most uncontroversial piece of evidence for Darwinism that proves beyond any doubt, in your mind, that Evolution is true?????

Timothee –

Darwinism/neo-Darwinism is a standard term used repeatedly throughout the secular scientific literature by the Darwinists themselves.

For a quick example, see “General Stress Response Regulator RpoS in Adaptive Mutation and Amplification in Escherichia coli” at http://www.genetics.org/cgi/content/full/166/2/669

The discussion there specifically talks about why they think the mutational process is within the bounds of neo-Darwinism. So, whether you agree or disagree with their arguments, it is obvious that neo-Darwinism is a valid scientific terminology which refers to a specific view of evolutionary change.

Might there be a subtle but important difference between “Darwinism” as a label for a theory (or, more precisely, for a family of theories) and “Darwinism” as a world-view, complete with metaphysics, ethics, and politics?

Timothee :

Tu es complètement dans le champs et quelqu’un qui croit avoir vu la vérité mais qui s’est fait avoir.

Tes infomations sont datées et erronées. Si tu crois que l’oeil, ou l’ATP synthase, ou les 247 nano machines qui travaillent en coordination dans l’ADN de la levure sont le produit de mutations non dirigées + sélection, ta crédulité frôle la follie et j’ai un très joli pont à te vendre pas cher!

Comme tous les Darwiniste fondamentaliste, tu es incapable de raisonner logiquement sur le sujet; tel que l’astronome Fred Hoyle a dit,

So it came about from 1860 onward that new believers became in a sense mentally ill, or, more precisely, either you became mentally ill or you quitted the subject of biology, as I had done in my early teens. The trouble for young biologists was that, with everyone around them ill, it became impossible for them to think they were well unless they were ill, which again is a situation you can read all about in the columns of Nature.

(Hoyle, F., “Mathematics of Evolution,” [1987], Acorn
Enterprises: Memphis TN, 1999, pp.3-4).

Tu démontre également une arrogance flagrante inappropriée pour tes faibles connaissances et ce qui me semble être un âge d’adolescence. Tu te prend pour qui au juste? Le grand scientifique qui va corriger William Dembski? Ne nous fait pas rire svp!

En passant, ton point de vue sur le flagellum et irreducible complexité est totalement enfantin. Bref, tu n’as rien compris du tout et tu ne regarde pas bien le fond des choses.

Pourtant tu viens ici en te croyant bon pour corriger ce que tu crois, de façon erronée, être des erreurs. C’est toi qui esà coté de la track.

Je te suggère de contempler ceci:
A scientific theory is an established and experimentally verified fact or collection of facts about the world. Unlike the everyday use of the word theory, it is not an unproved idea, or just some theoretical speculation. The latter meaning of a ‘theory’ in science is called a hypothesis. - http://www.whatislife.com/glossary/t.htm

en comparaison avec ceci:

“The history of organic life is undemonstrable; we cannot prove a whole lot in evolutionary biology, and our findings will always be hypothesis. There is one true evolutionary history of life, and whether we will actually ever know it is not likely. Most importantly, we have to think about questioning underlying assumptions, whether we are dealing with molecules or anything else.” Jeffrey H. Schwartz, Professor of Biological Anthropology, University of Pittsburgh, February 9, 2007 - mon emphase

Bien évidemment le néo-Darwinisme ne se tient même pas en tant que théorie valable. Même pas selon certains Darwiniste bien diplômés!

Alors “Two thumbs down for” you. Tu ne saisi rien de cette histoire.

Borne,

Ca me fait grand plaisir de lire, en français, une explication tellement lucide.

Gilbert (prononcé zheel-BER)

Timothee

First, A few thoughts on a single proteins complexity: Then, if you are interested, we may look at Dr. Behe’s work on the probability of just two various types of protein molecules binding together as required by Darwinian evolution;

The simplest living thing (bacteria) ever found on earth is constructed with (among other things) over a million protein molecules. Protein molecules are made from one dimensional sequences of the 20 different L-amino acids that can be used as building blocks for proteins. It is easily demonstrated mathematically that the entire universe does not even begin to come close to being old enough, nor large enough, to ally generate just one small but precisely sequenced 100 amino acid protein (out of the over one million interdependent protein molecules of longer sequences that would be required to match the sequences of their particular protein types) in that very first living bacteria. If any combinations of the 20 L-amino acids that are used in constructing proteins are equally possible, then there are (20100) =1.3 x 10130 possible amino acid sequences in proteins being composed of 100 amino acids. This impossibility, of finding even one “required” specifically sequenced protein, would still be true even if amino acids had a tendency to chemically bond with each other, which they don’t despite over fifty years of experimentation trying to get amino acids to bond naturally (The odds of a single 100 amino acid protein overcoming the impossibilities of chemical bonding and forming spontaneously have been calculated at less than 1 in 10125 (Meyer, Evidence for Design, pg. 75)). The staggering impossibility found for the universe ever generating a “required” specifically sequenced 100 amino acid protein by would still be true even if we allowed that the entire universe, all 1080 sub-atomic particles of it, were nothing but groups of 100 freely bonding amino acids, and we then tried a trillion unique combinations per second for all those 100 amino acid groups for 100 billion years! Even after 100 billion years of trying a trillion unique combinations per second, we still would have made only one billion, trillionth of the entire total combinations possible for a 100 amino acid protein during that 100 billion years of trying! Even a child knows you cannot put any piece of a puzzle anywhere in a puzzle. You must have the required piece in the required place! The simplest forms of life ever found on earth are exceedingly far more complicated jigsaw puzzles than any of the puzzles man has ever made. Yet to believe a naturalistic theory we would have to believe that this tremendously complex puzzle of millions of precisely shaped, and placed, protein molecules “just happened” to overcome the impossible hurdles of chemical bonding and probability and put itself together into the sheer wonder of immense complexity that we find in the cell.

Instead of us just looking at the probability of a single protein molecule occurring (a solar system full of blind men solving the Rubik’s Cube simultaneously), let’s also look at the complexity that goes into crafting the shape of just one protein molecule. Complexity will give us a better indication if a protein molecule is, indeed, the handi-work of an infinitely powerful Creator.
In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, that is 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it is estimated it will take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape. In real life, the protein folds into its final shape in a fraction of a second! The computer would have to operate at least 33 million times faster to accomplish what the protein does in a fraction of a second. That is the complexity found for JUST ONE “simple” protein. It is estimated, on the total number of known life forms on earth, that there are some 50 billion different types of unique proteins today. It is very possible the domain of the protein world may hold many trillions more completely distinct and different types of proteins. The simplest bacterium known to man has millions of protein molecules divided into, at bare minimum, several hundred distinct proteins types. These millions of precisely shaped protein molecules are interwoven into the final structure of the bacterium. Numerous times specific proteins in a distinct protein type will have very specific modifications to a few of the amino acids, in their sequence, in order for them to more precisely accomplish their specific function or functions in the overall parent structure of their protein type. To think naturalists can account for such complexity by saying it “happened by chance” should be the very definition of “absurd” we find in dictionaries. Naturalists have absolutely no answers for how this complexity arose in the first living cell unless, of course, you can take their imagination as hard evidence. Yet the “real” evidence scientists have found overwhelmingly supports the anthropic hypothesis once again. It should be remembered that naturalism postulated a very simple “first cell”. Yet the simplest cell scientists have been able to find, or to even realistically theorize about, is vastly more complex than any machine man has ever made through concerted effort !! What makes matters much worse for naturalists is that naturalists try to assert that proteins of one function can easily mutate into other proteins of completely different functions by pure chance. Yet once again the empirical evidence we now have betrays the naturalists. Individual proteins have been experimentally proven to quickly lose their function in the cell with random point mutations. What are the odds of any functional protein in a cell mutating into any other functional folded protein, of very questionable value, by pure chance?

“From actual experimental results it can easily be calculated that the odds of finding a folded protein (by random point mutations to an existing protein) are about 1 in 10 to the 65 power (Sauer, MIT). To put this fantastic number in perspective imagine that someone hid a grain of sand, marked with a tiny ‘X’, somewhere in the Sahara Desert. After wandering blindfolded for several years in the desert you reach down, pick up a grain of sand, take off your blindfold, and find it has a tiny ‘X’. Suspicious, you give the grain of sand to someone to hide again, again you wander blindfolded into the desert, bend down, and the grain you pick up again has an ‘X’. A third time you repeat this action and a third time you find the marked grain. The odds of finding that marked grain of sand in the Sahara Desert three times in a row are about the same as finding one new functional protein structure (from chance transmutation of an existing functional protein structure). Rather than accept the result as a lucky coincidence, most people would be certain that the game had been fixed.” Michael J. Behe, The Weekly Standard, June 7, 1999, Experimental Support for Regarding Functional Classes of Proteins to be Highly Isolated from Each Other

“Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed – along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

Thimotee:

Your rather dogmatic affirmations deserve very long answers, but for the moment I would like only to clarify a fundamental misunderstanding about the flagellum and Behe’s IC, becuse you, like others, go on repeating, after Miller, the false concept that IC of the flagellum has been refuted. I’ll try to keep it simple (and yes, I have read the paper to which Miller refers).

The discussions about homologies, more or less strict, of some proteins of the flagellum to others of T3SS pump or of any other existing molecular machine are very debatable (indeed, any discussion about homologies is totally debatable) and completely irrelevant to the concept of IC. All so called answers to Behe’s formidable concept of IC seem to be completely unaware that IC is about the realistic credibility of a causal mechanism. So, to refute the IC of the flagellum, correctly affirmed by Behe, any darwinist should succeed in showing a sufficiently detailed and credible causal mechanism which can have produced the flagellum. In other words, something like that:

1) Let’s start form an organism, a bacterium, which has no flagellum, but has, for instance, the pump wich is supposed to have produced, evolutionarily speaking, the flagellum. Let’s call this bacterium A.

2) Let’s consider the final goal, that is a bacterium which has the flagellum. Let’s call that B.

3) Now, let’s calculate, even approximately, the modifications which can bring from A to B, and express them in number of necessary point mutations (or, if you don’t like mutations, in number of any given single random event you like, be it gene duplication, inversion, deletion, or any other thing). Let’s call every single random event which is necessary to go from A to B a “genetic bit”. Plese note that, even if the model is not completely detailed, it should be realistic enough to account for the transformation from the A genome to the B genome, at least as far as a fully functional flagellum is concerned.

4) Now, let’s divide the transition in any number of intermediate states.

The model will be successful in refuting the IC of the flagellum if, and only if:

a) Each intermediate state differs from the previous and the following one for a number of “genetic bits” small enough not to face unsurmountable probabilistic difficulties (in other words, no more than a dew unrelated mutations are allowed, probably no more than two or three, but we can be more generous, if you need)

b) Each intermediate state is specifically selectable because of a distinct functional advantage, capable of giving a reproductiove advantage and therefore a sufficient expansion of the mutated clone (here, unfortunately, we cannot be generous, distinct functional advantage must be present at each selected step).

In my knowledge, nobody has ever even vaguely attempted to refuted the IC of the flagellum (or of any other IC structure) in this way.

Please note that I am not asking too much. I am not asking, for example, that such a model be “proven” as real. I will be satisfied with a theoric model, provided it is detailed enough, credible, and quantitavely analyzed at the molecular level.

Furthermore, I am not asking that the increased function of each intermediate state be the same as the final (or initial) function. Any form of the mythological “cooption” is allowed, provided that the coopted functions are demonstrated and that their molecular derivation from other functions in terms of a very small number of “genetic bits” be verified.

I am, anyway, asking that the model eaxplain all the necessary molecular changes in as much detail as reasonalbly possible, and that it include not only the changes in the effector genes (the proteins), but also all the new regulatory and assembling functions, at least as far as we can understand a minimum of them (for instance, the necessay regulations of transcription, the correct rate, the temporal sequence, and so on). I understand that almost nothing is known of these matters, and therefore I would be happy, in a first moment, with the explanation of the modifications in the final proteins, but let’s remember that, probably, the greatest impossibilities are to be found in the “evolution” of the new regulatory network.

In the light of what above said, I can confidently affirm:
nobody, and I mean nobody, has in any way refuted the irreducible complexity of the flagellum, as shown by Behe.

Dave,

I believe Nick Matzke made a fatal error by saying that the flagellum existed in the very distant past. Such an admission limits the potential origin of the proteins from other pathways and makes the co-option arguments even more nonsensical.

So if the proteins exist in other pathways, the logical conclusion is that are descended from the flagellum and not used to somehow magically build up the flagellum.

Timothee, if you are still there and understand these arguments, then you might want to comment on them.

@jerry:

Hopefully I will find the time to anwser the most interesting of them…

Hopefully we can engage on a debate on the flagellum as well. With a bunch of friends of mine, we usually use google docs to write dialogues for our respective blogs, this could be doable here as well…

The presence of a single protein in several pathways or structure means that complexity is in fact reduced: complex structures are built by assembling small parts, each one having a “unique” function.

I could cheat on you by saying that the assembly problem could be solved by probabilities… I think that the complex could be assembled not step-by-step, but (step-by-step)-by-(step-by-step): parts are assembled separately, and bigger parts assembles together to make the flagellum. It’s only an hypothesis.

The problem with your “mouse trap argument” is that assembling molecules is not at all like assembling metal parts. That’s chemistry. You don’t need to “clip” proteins or molecules together to keep them attached (look at the immune complexes, for example).

As for the paper: a scientific paper is never grandiose. Saddly, because some of them are actually big landmarks.

@StephenB:

I’m not a sociologist, I can think by myself :p

I think that interactions between species played a great role in evolution (and still continue to do so, but you need very accurate experiments and analysis to show it). In fact I’m pretty sure of that, because of my readings/experiments.

On a more “molecular” basis, I haven’t read enough litterature to claim my “allegiance” to a model – the fields of complxity vs evolvability is of great interest, but difficult to approach.

I’me close to SJG, but I won’t follow him on each point. As I won’t follow Kimura, Darwin, Maynard-Smith, or anybody else…

My scientific vision, on a more “day to day” basis, is to stick to the fact, make as many hypothesis as I can, try to analyse the facts, see which hypothesis is closer, try to find a way to demonstrate, make more subtle hypothesis, and so on. I’m much more confident in experimentation than in anything else.

@DaveScot (#13):

According to your PS I will say that you’ve missed a point on evolution. Anybody never said than a bacteria will become a baboon. Nor than a monkey will become (or already have became) a man. That’s a common misconception anyway. We just share common ancestors.

Plus, I don’t see the point of your “experiment”. It’s the very principle of DNA to mutate. I just stressed out the fact that evolution couldn’t be reduced to mutation.

As for your PPS : I would be sorry if you choose to end the debate here…

@bornagain77:

I don’t seek evidences for “darwinism”. I seek evidences for “evolution” (Darwinism is a model to explain a fact, the fact being evolution).

I have a lot of them. What do you think of apparition of resistance to parasites, modification of sexual ornaments in presence of predators, for a starter?

@Carl Sachs : Yes. darwinism is a label for a theory. It’s not anything else. NS doesn’t apply to ethics, politics, economics, the movie industry, or anything else.

@Borné:

Merci de me permettre ce switch vers une langue que je maîtrise bien plus que l’anglais…

Je n’ai pas dit que la mutation n’est pas dirigée. Laisse moi t’expliquer. Elle n’est juste pas dirigée ex ante, par une force ou intervention divine. Elle est dirigée ex post, par les possibilités adaptatives qu’elle confère. Si l’apparition d’une nouvelle fonction représente un avantage, alors il y a de fortes chances qu’elle soit conservée, par un simple phénomène de sélection. Ou qu’elle permette une migration, et que le nouvel environnement soit porteur de nouvelles pressions, et ainsi de suite…

Il suffit de comprendre qu’une grande parties des mutations étant délétères, celles qui restent sont neutres ou bénéfiques. Si l’évolution n’est pas finaliste, elle est néanmoins finalisante; ne nous engageons pas dans un débat sur ce genre de notions, je ne suis pas certain qu’il aie sa place ici, surtout dans la langue de Molière. Si tu veux en lire plus (en français), fais toi plaisir.

Je ne me lancerai pas dans un cours d’évolution, je n’ai pas vocation à ça.

Je ne relève pas la citation de Hoyle, n’étant pas visé car ni Darwiniste “pur et dur”, ni fondamentaliste.

En revanche, j’apprécierai que tu ne présume pas de mes connaissances, ni même de mon âge. Je te l’accorde, cependant, il est assez peu élevé. Beaucoup plus faible que la moyenne de mon amphi, même. J’apprécierai beaucoup de corriger Dembski en tant que scientifique (Shallit n’a pas manqué de dire tout le bien qu’il pensait de ses travaux mathématiques récemment), le problème étant que je ne m’avance pas sur le terrain de la pseudo-science. Et Dembski me laisse assez indifférent, en fait. Sauf qu’il a récupéré une bourse de 40000$ annuels, ce qui fait baver d’envie n’importe quel étudiant.

Concernant ta définition de la théorie scientifique, elle n’est jamais (et c’est même marqué dans le disclaimer du site) que celle de son auteur…

@BornAgain77:

I know probabilities. I also know that some amino-acids are mote likely to get involved in some structures than others. Some sequence are known to adopt a single conformation in space. And so on. Plus the HSPs.

Dave,

You have mentioned before that hundreds of research scientists support ID but since many journals are controlled by the Darwinists, they have trouble getting published.

Have they been approached about publishing in PCID?. That would seem to be the ideal venue for getting the word out. In fact, I wonder why Dr. Dembski and Dr. Marks did not choose this journal for publishing the work of the EIL.

Also, has the PCID page been updated recently? It shows the last issue as being in July 2005. I would think that there would be a lot more research out there to publish.

@larrycranston:

why not in PLoS One? It’s an open access journal, after all, with very little peer-review (but evaluation of papers post-publication and possibility to comment)

As long as they answered the questions too the best of their ability I really don’t get the fuss.

Timothee,
I have to agree with Borné.
your comments seem to indicate that you do not understand the objections of ID to naturalistic evolution.
You said that a baboon evolving from a bacteria was a misconseption, instead they share a common ancestor. This is so retorical, circular, and sounds like my HS teachers and undergrad professors. The common ancestor is a bacteria-like organism, that baboons, humans evolved from. I will let others who know more than myself discuss irreducible complexity, but even I can see the foolishness in this comment about common ancestor misconceptions.

gehman:

“This is so retorical, circular, and sounds like my HS teachers and undergrad professors. The common ancestor is a bacteria-like organism, that baboons, humans evolved from.”

Touché. You are perfectly right. That’s the problem with darwinian “arguments”: you never get a true answer when you make specific objections, only retorical, vague or self-referential discussions, or just the conformistic referral to established authority.
I can understand the reason, it’s really difficult to defend a theory which has no sense, but it’s depressing anyway. I like confrontation, but how can you have confrontation with such an insubstantial way of thinking?

I had already noticed, on darwinian fields, this kind of specious argument about common ancestors, as though speaking of a common ancestor eliminates the ridicule idea of the transformation, for instance, fron a bacterium to a mammal or any other, forgetting that the supposed common ancestor if often a purely virtual entity, or anyway is similar to something that we can observe today. However we put it, if one believes in darwinian evolution, in any variant, one has to believe that every present livng being derives fron something like a bacterium or archea, or from even simpler, fairy tale forms of life which have never been observed in any direct or indirect way.

It seems to me the same kind of retorical argumentation as when they say that it is wrong to focus only on random mutation, because other factors like genetic drift, gene duplications and similar are more impotant, forgetting the point of ID is completely independent from the kind of “random” change one prefers to assume as the graet driving engine of information building: in terms of information andprobability, any random modification is equivalent, be it a point mutation, or a deletion, or a gene duplication; any random event has the same chance to contribute to new significant information building, which is almost nil.

Timothee:

I think that the complex could be assembled not step-by-step, but (step-by-step)-by-(step-by-step): parts are assembled separately, and bigger parts assembles together to make the flagellum. It’s only an hypothesis.

If evolution advances, per Darwinism, step-by-step, then for the 40 or so proteins in the bacterial flagellum, 40 positive/beneficial steps that need to be taken to assemble it. Now, let’s say we consider pairs. Then you have 20 steps needed to bind each of twenty pairs together. These twenty pairs must in turn attach to one another. That’s another 20 steps. Total positive/beneficial steps needed? 40. Do the analysis with three per group, or four. It doesn’t change a blessed thing. The only thing that would help your cause is if these “pairs”, or “triplets”, or “quadruplets” already exist in the cell. Yes, that’s right, we need……”intermediate forms”. (Just as a reminder, we don’t find them in the fossil record)

You might want to re-think your hypothesis.

Timothee:

I can, however, see something like a structural role, or the presence of very distal elements, or elements involved in chemical regulation of chromatid structure. We don’t need to invoke a designer here. We need to carry out good science. Then find out.

Who said anything about a Designer? Remember, we’re talking about “dogmatism”. There are experiments showing that parts of so-called “junk DNA” are highly-conserved, yet that have no known function. This is a clear violation of basic neo-Darwinian assumptions. Why, then, don’t you begin to question neo-Darwinian thought? Is it because Darwinism/neo-Darwinism MUST be true? But is that science, or “dogmatism”?

You express confidence that “junk-DNA” will all be figured out in 5 years. First, this is unbridled optimism on your part. Second, I suspect that over the years they will come to find out in a deeper way than is already known the extreme complexity of the regulatory mechanisms involved in organismal development. What will be seen is a type of computer coding system of unparalleled complexity. Now, if that turns out to be the case, are you going to: (1) assume that a coding system of greater complexity than mankind has ever seen came about by chance, or (2) decide that it is the work of guided intelligence. If it turns out to be the former, the chance scenario, you will be doing so in the complete absence of anything similar happening in our world. It will amount to complete supposition on your part. Do you call that “science”? Remember, you said it yourself, science isn’t facts, it’s a way of coming to know facts. So, will this be your “way” of coming to know facts: assuming a mechanism that has never been seen to operate. (What we see in biology, of course, can’t be used to defend any hypothesis since it is the very thing we’re trying to explain.) How will you get yourself out of this dilemna?

About Wikipedia : that’s not an encyclopedia. Don’t believe, it’s crappy. Trust me one this one, I used to wrote articles in it

I don’t understand: are you saying we shouldn’t believe the things you write? More seriously, the obvious point of referring to Wikipedia is to show that our use of Darwinism has nothing to do with stigmatizing those who presume that Darwinian theory explains biological complexity; we use it only to identify them. No matter what term we use, they don’t seem to like it. They seem to be irritated if we use any label of any kind. Yet, whether someone is a Jew, a Christian, an atheist, a Moslem, a Catholic, if you support the contentions of ID, you are quickly labeled a “creationist” by the other side. I’m wondering, since you’re so concerned about labels of these types, are you now going to tell your Darwinist friends not to call us “creationists”? Somehow I doubt that.

These ripostes are fun, but they remind me of some advice I received from a friend many years ago–”Don’t shoot the skinny rabbits.”

It would be nice if a generous benefactor could be found for an ID journal, perhaps along the lines of “First Things,” where the type of information and argument seen here could be shared with a thirsy public.

I’m quite sure that a well-written journal of this type would find a ready audience, not only because the design story is quite appealing in its own right, but also because it provides a fresh alternative to the stagnation seen in Big Science and the lockstep formalism of “Nature” et al.

The bad news for “timothee” is that he now represents the Establishment and must carry the Establishment’s baggage. This can be seen in the assertion that science is not knowledge but perpetual process–pure resistance to the limitations of observation–which reflects the fealty of Modern Science to theory.

The theorists cannot be the radicals and prophetic free spirits that they want to be when Theory has been normalized. They must protect the norm, and therefore they wind up sounding like scolds.

Design is the new naughty boy in science, and it seems that now is the time to play.

allanius:

I second your proposition for a journal.

Just for the anglophones (english speakers) here, timothee says in his response to me:

I would really appreciate correcting Dembski as a scientist (Shallit didn’t miss saying all the good he thought about his mathematics recently) the problem being that I’m not going into the terrain of pseudo-science. And Dembski leaves me indifferent. Accept that he gets a 40000$ annual bursery, which is enough to make any student drool with envy.

Apparently our young snotty timothee is unwilling to admit his real level of understanding isn’t anywhere near as deep as he lets on.

He also twists my user name into a word meaning, willfully and annoyingly close-minded or narrow-minded.

Of course that’s like me calling Larry Moran, “Moron” (which of course he is) but not a good debate practice.

I don’t know about the others here but it seems obvious to me that our timothee is a young naive and pretentious student. Correct me if I’m wrong.

PaV: “I don’t understand: are you saying we shouldn’t believe the things you write?” Now theres a rebuttal that requires a good ROTFLMAO.

Now timothee: you say, “Je n’ai pas dit que la mutation n’est pas dirigée. Laisse moi t’expliquer. Elle n’est juste pas dirigée ex ante, par une force ou intervention divine. Elle est dirigée ex post, par les possibilités adaptatives qu’elle confère. Si l’apparition d’une nouvelle fonction représente un avantage, alors il y a de fortes chances qu’elle soit conservée, par un simple phénomène de sélection.”

Which, being translated, is, “I didn’t say that a mutation wasn’t directed. … It just isn’t directed ex ante, by a divine force or intervention. It is directed ex post, by the adaptive possibilities that it confers. If the appearance of a new function represents an advantage then the chances are strong that it will be conserved by a simple selection phenomena.”
Now what I seem to be reading here is that you affirm that there is no divine force or intervention in a mutation - granted. Mutations are notoriously deleterious or useless and are the major cause of disease- Bugs in the code.

Then you repeat the Darwinian mantra that selection just weeds out the bad and keeps the good.

How impressive.

Then you add, “It’s sufficient to understand that a large part of mutations are noxious, those that remain are neutral or beneficial.”

Sorry. I fail to see where you’re saying anything useful to your cause - which seems to be to correct IDists by preaching to them what they already know!

Also the majority of mutations are “noxious” (and many Darwinists are obnoxious). Few are beneficial and the odds of the beneficial ones overtaking or even surviving the deleterious are practically null.

Timothee;
You stated as proof of evolution:

What do you think of apparition of resistance to parasites, modification of se^xual ornaments in presence of predators, for a starter?

Ok Timothee; Do you want to explain why this “suggestive micro-evolutionary” evidence builds information on the molecular level as required for a successful evolutionary scenario?

It is commonly known that all anti-biotic resistance is acquired by loss of preexisting molecular function thus obeys Genetic Entropy, my confident hunch is that your resistance to parasites falls in this category (Sanford: 2005)

I guess the modification of se^xual ornaments in the presence of predators is referring to some phenomena similar to in which peacocks or some other animal with flashy bells and whistles for the females gets eaten more than his less flashy brethren in the presence of predators,,,Thus once again you have not demonstrated the gain in genetic information but merely a restriction of preexisting information…
I find your treatment of the evidence contemptible and suggest you brush up real hard on molecular biology before you make such shallow assertions for evidence of evolution on this site!!!!!

It is commonly known that all anti-biotic resistance is acquired by loss of preexisting molecular function thus obeys Genetic Entropy,…

All? What about penicillin resistance? That seems to be due to a gain in function (i.e. in production of beta-lactamase or penicillinase) or a modification of binding sites.

Bob

Pav and allanius:

There is such a journal. If you look at my post above, or follow the ISCID link to the right, you will find a page for the journal PCID. However, as I also noted above, there does not appear to be any issues since 2005.

I still don’t know if there are more issues and the page needs to be updated or if the journal stoppped publishing for some reason.

Timothee wrote: “T3SS, plus the fact that 40 out of 42 proteins are used in other pathways, for a starter.”

Checking my calendar to make sure it’s not April 1 . . .

Bob O’H

# The enzyme penicillinase, produced by some bacteria, destroys penicillin. If a member of a bacterial strain producing a modest amount of this substance were to inherit a mutational defect which damaged or deleted the gene controlling production of this enzyme, the organism would invest a lot of resources into producing copious amounts of penicillinase. Thus, this defect would be an advantage in an environment containing penicillin, but would be a disadvantage otherwise. Once again, a loss is involved. There is no evidence that the complex information coding for penicillinase production arose by mutation.

# For a somewhat more detailed and technical treatment of the whole matter of antibiotic resistance, with further references, see also C. Wieland, ‘Antibiotic Resistance in Bacteria’, CEN Technical Journal 8(1):5–6, 1994.

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